Pseudomonas putida 06909 genes expressed during colonization on mycelial surfaces and phenotypic characterization of mutants

AIMS: The main focus of this study was to gain an overall view of Pseudomonas putida 06909 genes involved in the Pseudomonas-Phytophthora interaction as a biological control mechanism, and to understand the roles of these genes. METHODS AND RESULTS: Sixteen Ps. putida genes with increased expression on Phytophthora mycelial surfaces were identified using in vivo expression technology (IVET) screening. Sequence analysis of these Phytophthora mycelium-induced (pmi) genes revealed that many of them display similarity to genes known or predicted to be involved in carbohydrate catabolism, energy metabolism, amino acid/nucleotide metabolism, and membrane transport processes. Disruption of three pmi genes encoding succinate semialdehyde dehydrogenase, a dicarboxylic acid transporter, and glyceraldehyde-3-phosphate dehydrogenase showed significant phenotypic differences involved in the colonization processes, including motility, biofilm formation on abiotic surfaces, colony morphology, and competitive colonization of fungal mycelia. All three of these pmi genes were induced by glycogen and other substances, such as organic acids and amino acids utilized by Ps. putida. CONCLUSIONS: The IVET screening and mutant characterization can be used to identify bacterial genes that are induced on the mycelial surface and provide insight into the possible mechanisms of mycelial colonization by this bacterium. SIGNIFICANCE AND IMPACT OF THE STUDY: The IVET screening through a bacterial genome library might be a huge task. However, because the genes involved in direct interaction with Phytophthora and in bacterial adaptation can be identified, the IVET system will be a valuable tool in studying biocontrol bacteria at the molecular and ecological levels.     

Towards genetic markers in animal populations as biomonitors for human-induced environmental change

Genetic markers provide potentially sensitive indicators of changes in environmental conditions because the genetic constitution of populations is normally altered well before populations become extinct. Genetic indicators in populations include overall genetic diversity, genetic changes in traits measured at the phenotypic level, and evolution at specific loci under selection. While overall genetic diversity has rarely been successfully related to environmental conditions, genetically based changes in traits have now been linked to the presence of toxins and both local and global temperature shifts. Candidate loci for monitoring stressors are emerging from information on how specific genes influence traits, and from screens of random loci across environmental gradients. Drosophila research suggests that chromosomal regions under recent intense selection can be identified from patterns of molecular variation and a high frequency of transposable element insertions. Allele frequency changes at candidate loci have been linked to pesticides, pollutants and climate change. Nevertheless, there are challenges in interpreting allele frequencies in populations, particularly when a large number of loci control a trait and when interactions between alleles influence trait expression. To meet these challenges, population samples should be collected for longitudinal studies, and experimental programmes should be undertaken to link variation at candidate genes to ecological processes.     

Invasiveness in plant communities with feedbacks

The detrimental effects of invasive plant species on ecosystems are well documented. While much research has focused on discovering ecological influences associated with invasiveness, it remains unclear how these influences interact, causing some introduced exotic species to become invasive threats. Here we develop a framework that incorporates the influences of propagule pressure, frequency independent growth rates, feedback relationships, resource competition and spatial scale of interactions. Our results show that these ecological influences interact in complex ways, resulting in expected outcomes ranging from inability to establish, to naturalization, to conditional invasion dependent on quantity and spatial distribution of propagules, to unconditional takeover. We propose a way to predict the likelihood of these four possible outcomes, for a species recently introduced into a given target community. Such information could enable conservation biologists to craft strategies and target remediation efforts more efficiently and effectively in order to help maintain biodiversity in ecological communities.     

The relationship between dispersal ability and geographic range size

There are a variety of proposed evolutionary and ecological explanations for why some species have more extensive geographical ranges than others. One of the most common explanations is variation in species' dispersal ability. However, the purported relationship between dispersal distance and range size has been subjected to few theoretical investigations, and empirical tests reach conflicting conclusions. We attempt to reconcile the equivocal results of previous studies by reviewing and synthesizing quantitative dispersal data, examining the relationship between average dispersal ability and range size for different spatial scales, regions and taxonomic groups. We use extensive data from marine taxa whose average dispersal varies by seven orders of magnitude. Our results suggest dispersal is not a general determinant of range size, but can play an important role in some circumstances. We also review the mechanistic theories proposed to explain a positive relationship between range size and dispersal and explore their underlying rationales and supporting or refuting evidence. Despite numerous studies assuming a priori that dispersal influences range size, this is the first comprehensive conceptual evaluation of these ideas. Overall, our results indicate that although dispersal can be an important process moderating species' distributions, increased attention should be paid to other processes responsible for range size variation.     

Effects of rangeland management on the site occupancy dynamics of prairie-chickens in a protected prairie preserve

We investigated the site occupancy dynamics of greater prairie-chickens at Konza Prairie Biological Station, a protected site in northeastern Kansas that is managed for ecological research. We surveyed the site during mid-Mar to mid-May, 1981–2008, and recorded detections of birds in a grid of 6.3 ha survey plots (n = 187 plots). We used multiseason occupancy models to estimate the probabilities of occupancy (ψ) and detection (p), and tested whether land cover in woody vegetation, and land use with prescribed fire or grazing management influenced the dynamic processes of site colonization and local extinction. Probability of detection per site was consistently <1 and varied among years (p = 0.12–0.82). Site occupancy of prairie-chickens declined 40% over the study period from a high of ψ = 0.19 ± 0.02 SE in 1981 to a low of 0.11 ± 0.03 in 2008, despite protection from disturbance at leks and losses to harvest. We found that different sets of environmental factors impacted the probabilities of colonization and local extinction. Probability of colonization for an unoccupied site was negatively associated with the proportion of site occupied by woodland cover (β = −1.25), and was lower for grazed sites (β = −0.62). In contrast, probability of local extinction was affected by a weak interaction between grazing and average frequency of prescribed fire (β = −1.01), but model-averaged slope coefficients were not statistically different than 0. To conserve prairie-chickens, we recommend prairies be managed with combinations of prescribed fire and grazing that maintain a heterogeneous mosaic of prairie habitats, while preventing woody encroachment. To assess biotic responses to land management practices, field sampling should be based on occupancy models or similar techniques that account for imperfect detection. © 2011 The Wildlife Society.     

The role of ecological constraint in driving the evolution of avian song frequency across a latitudinal gradient

Just as features of the physical and biotic environment constrain evolution of ecological and morphological traits, they may also affect evolution of communication systems. Here we analyze constraints on rates of vocal evolution, using a large dataset of New World avian sister taxa. We show that species breeding in tropical forests sing at generally lower frequencies and across narrower bandwidths than species breeding in open habitats, or at high latitudes. We attribute these restrictions on birdsong frequency to the presence of high-frequency insect noise and greater degradation of high-frequency sounds in tropical forests. We fit Ornstein-Uhlenbeck models to show that recent evolution of song frequency has been more greatly constrained in tropical forests than elsewhere, that is, songs have shown less tendency to diverge over time in tropical forests, consistent with inferred acoustic restrictions. In addition, we find that song frequency has evolved more rapidly overall at high latitudes in both forest and open habitats. Besides a larger available sound window, other factors contributing to more rapid divergence at high latitudes may include an overall increased intensity of sexual selection, occupation of more divergent habitats, and the presence of fewer competing species.     

Microevolution of S-allele frequencies in wild cherry populations: respective impacts of negative frequency dependent selection and genetic drift

Negative frequency dependent selection (NFDS) is supposed to be the main force controlling allele evolution at the gametophytic self-incompatibility locus (S-locus) in strictly outcrossing species. Genetic drift also influences S-allele evolution. In perennial sessile organisms, evolution of allelic frequencies over two generations is mainly shaped by individual fecundities and spatial processes. Using wild cherry populations between two successive generations, we tested whether S-alleles evolved following NFDS qualitative and quantitative predictions. We showed that allelic variation was negatively correlated with parental allelic frequency as expected under NFDS. However, NFDS predictions in finite population failed to predict more than half S-allele quantitative evolution. We developed a spatially explicit mating model that included the S-locus. We studied the effects of self-incompatibility and local drift within populations due to pollen dispersal in spatially distributed individuals, and variation in male fecundity on male mating success and allelic frequency evolution. Male mating success was negatively related to male allelic frequency as expected under NFDS. Spatial genetic structure combined with self-incompatibility resulted in higher effective pollen dispersal. Limited pollen dispersal in structured distributions of individuals and genotypes and unequal pollen production significantly contributed to S-allele frequency evolution by creating local drift effects strong enough to counteract the NFDS effect on some alleles.     

Crop size as an index of chick provisioning in the Greater Flamingo Phoenicopterus roseus

After being fed by their parents, Greater Flamingo chicks store food in their crops, which protrude outwards. We allocated the crop profiles of chicks to four categories to assess the relationship between body mass and crop profile variation, and so determine whether crop size can be used as an accurate index of the amount of food ingested, and to determine the timing and frequency of provisioning. We registered changes in body mass and crop fullness in eight chicks captured with turgid crops and kept in captivity until constant mass was achieved. The meal mass ingested by the chicks during each parental feeding was around 18% of net chick mass and varied greatly with crop profile. Mean transition times between the four crop profile categories ranged from 6 to 14 h. Between 1998 and 2009, 34% of chicks caught for ringing in a breeding colony had empty crops. From crop profiles recorded during the handling of chicks, it was estimated that approximately one‐third of the chicks were fed in the evening and another third during the night. Our results have implications for the estimation of body condition indexes because body mass should be free of the influence of the mass of the food in the crop.     

The role of disjunction and postglacial population expansion on phylogeographical history and genetic diversity of the circumboreal plant Chamaedaphne calyculata

In the last decade a number of studies has illustrated quite different phylogeographical patterns amongst plants with a northern present‐day geographical distribution, spanning the entire circumboreal region and/or circumarctic region and southern mountains. These works, employing several marker systems, have brought to light the complex evolutionary histories of this group. Here I focus on one circumboreal plant species, Chamaedaphne calyculata (leatherleaf), to unravel its phylogeographical history and patterns of genetic diversity across its geographical range. A survey of 29 populations with combined analyses of chloroplast DNA (cpDNA), internal transcribed spacer (ITS) and AFLP markers revealed structuring into two groups: Eurasian/north‐western North American, and north‐eastern North American. The present geographical distribution of C. calyculata has resulted from colonization from two putative refugial areas: east Beringia and south‐eastern North America. The variation of chloroplast DNA (cpDNA) and ITS sequences strongly indicated that the evolutionary histories of the Eurasian/north‐western North American and the north‐eastern North American populations were independent of each other because of a geographical disjunction in the distribution area and ice‐sheet history between north‐eastern and north‐western North America. Mismatch analysis using ITS confirmed that the present‐day population structure is the result of rapid expansion, probably since the last glacial maximum. The AFLP data revealed low genetic diversity of C. calyculata (P = 19.5%, H = 0.085) over the whole geographical range, and there was no evidence of loss of genetic diversity within populations in the continuous range, either at the margins or in formerly glaciated and nonglaciated regions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 761–775.